Compositions and methods for determining likelihood of an increased susceptibility to contracting Johne's disease

Abstract

Collections of polynucleotides useful for estimating breeding value or detecting likelihood of an increased susceptibility to contracting paratuberculosis are disclosed. The polynucleotides are used to detect genomic sequences quantitatively associated with an increased susceptibility to contracting paratuberculosis. Methods for using the collections to estimate breeding value or predict likelihood of an increased susceptibility to contracting paratuberculosis are also provided. Kits comprising the collection of polynucleotides are also provided.

We claim: 
     
       1. A method of prophylactically treating paratuberculosis in a population of cattle, comprising the steps of:
 1) genotyping a biological sample obtained from one or more members of the cattle population, and detecting a genotype selected from the group consisting of: 
 (a) SNP BTA-72108-no-rs T/C, wherein one copy of BTA4 comprises SEQ ID NO: 149, and the other copy of BTA4 comprises SEQ ID NO: 149 wherein the 61st nucleotide base is T; 
 (b) SNP BTA-116871-no-rs T/C, wherein one copy of BTA17 comprises SEQ ID NO:32, and the other copy of BTA17 comprises SEQ ID NO:32 wherein the 61st nucleotide base is T; 
 (c) SNP ARS-BFGL-NGS-41833 T/G, wherein one copy of BTA20 comprises SEQ ID NO:76, and the other copy of BTA20 comprises SEQ ID NO:76 wherein the 61st nucleotide base is T; 
 (d) SNP ARS-BFGL-NGS-75935 T/C, wherein one copy of BTA21 comprises SEQ ID NO: 173, and the other copy of BTA21 comprises SEQ ID NO: 173 wherein the 61st nucleotide base is T; 
 (e) SNP BTA-28297-no-rs G/G, wherein both copies of BTA10 comprise SEQ ID NO:86; 
 (f) SNP BTA-60642-no-rs A/A, wherein both copies of BTA25 comprise SEQ ID NO:89 wherein the 61st nucleotide base is A; 
 (g) SNP UA-IFASA-8974 A/A, wherein both copies of BTA20 comprise SEQ ID NO:53 wherein the 61st nucleotide base is A; 
 (h) SNP BTB-01112664 T/T, wherein both copies of BTA2 comprise SEQ ID NO: 141 wherein the 61st nucleotide base is T; 
 (i) SNP BTB-00261837 T/T, wherein both copies of BTA6 comprise SEQ ID NO: 14 wherein the 61st nucleotide base is T; 
 (j) SNP BTA-116871-no-rs T/T, wherein both copies of BTA17 comprise SEQ ID NO:32 wherein the 61st nucleotide base is T; 
 (k) SNP Hapmap54042-ss46526396 A/A, wherein both copies of BTA22 comprise SEQ ID NO: 13 wherein the 61st nucleotide base is A; 
 (l) SNP ARS-BFGL-NGS-115504 A/A, wherein both copies of BTA25 comprise SEQ ID NO:60 wherein the 61st nucleotide base is A; 
 (m) SNP ARS-BFGL-NGS-109845 T/T, wherein both copies of BTA29 comprise SEQ ID NO: 164 wherein the 61st nucleotide base is T; 
 (n) SNP Hapmap26742-BTA-156593 A/A, wherein both copies of BTA17 comprise SEQ ID NO: 176 wherein the 61st nucleotide base is A; or 
 (o) SNP ARS-BFGL-NGS-103845 T/C, wherein one copy of BTA7 comprises SEQ ID NO: 146, and the other copy of BTA7 comprises SEQ ID NO:146 wherein the 61st nucleotide base is T; and 
 2) either: 
 (a) selectively breeding together two or more members of the cattle population that were genotyped in step 1) as SNP BTA-72108-no-rs T/C, SNP BTA-116871-no-rs T/C, SNP ARS-BFGL-NGS-41833 T/G, SNP ARS-BFGL-NGS-75935 T/C, SNP BTA-28297-no-rs G/G, or SNP BTA-60642-no-rs A/A; or 
 (b) screening for the presence of  Mycobacterium avium , ssp.  paratuberculosis  (MAP) or physically separating from the cattle population any of the one or more members of the cattle population that were genotyped in step 1) as SNP UA-IFASA-8974 A/A, SNP BTB-01112664 T/T, SNP BTB-00261837 T/T, SNP BTA-116871-no-rs T/T, SNP Hapmap54042-ss46526396 A/A, SNP ARS-BFGL-NGS-115504 A/A, SNP ARS-BFGL-NGS-109845 T/T, SNP Hapmap26742-BTA-156593 A/A, or SNP ARS-BFGL-NGS-103845 T/C; 
 whereby paratuberculosis in the cattle population is prophylactically treated. 
 
     
     
       2. The method of  claim 1 , wherein in step 2)(b), any of the one or more members of the cattle population that were genotyped in step 1) as SNP UA-IFASA-8974 A/A, SNP BTB-01112664 T/T, SNP BTB-00261837 T/T, SNP BTA-116871-no-rs T/T, SNP Hapmap54042-ss46526396 A/A, SNP ARS-BFGL-NGS-115504 A/A, SNP ARS-BFGL-NGS-109845 T/T, SNP Hapmap26742-BTA-156593 A/A, or SNP ARS-BFGL-NGS-103845 T/C are screened for the presence of MAP. 
     
     
       3. The method of  claim 2 , further comprising the step of physically separating from the cattle population any of the one or more members of the cattle population that were genotyped in step 1) as SNP UA-IFASA-8974 A/A, SNP BTB-01112664 T/T, SNP BTB-00261837 T/T, SNP BTA-116871-no-rs T/T, SNP Hapmap54042-ss46526396 A/A, SNP ARS-BFGL-NGS-115504 A/A, SNP ARS-BFGL-NGS-109845 T/T, SNP Hapmap26742-BTA-156593 A/A, or SNP ARS-BFGL-NGS-103845 T/C and found through the screening of step 2)(b) to be positive for the presence of MAP. 
     
     
       4. The method of  claim 1 , wherein in step 2)(b), any of the one or more members of the cattle population that were genotyped in step 1) as SNP UA-IFASA-8974 A/A, SNP BTB-01112664 T/T, SNP BTB-00261837 T/T, SNP BTA-116871-no-rs T/T, SNP Hapmap54042-ss46526396 A/A, SNP ARS-BFGL-NGS-115504 A/A, SNP ARS-BFGL-NGS-109845 T/T, SNP Hapmap26742-BTA-156593 A/A, or SNP ARS-BFGL-NGS-103845 T/C are physically separated from the cattle population. 
     
     
       5. The method of  claim 4 , wherein before the one or more members of the cattle population that were genotyped in step 1) as SNP UA-IFASA-8974 A/A, SNP BTB-01112664 T/T, SNP BTB-00261837 T/T, SNP BTA-116871-no-rs T/T, SNP Hapmap54042-ss46526396 A/A, SNP ARS-BFGL-NGS-115504 A/A, SNP ARS-BFGL-NGS-109845 T/T, SNP Hapmap26742-BTA-156593 A/A, or SNP ARS-BFGL-NGS-103845 T/C are physically separated from the cattle population, these one or more members of the cattle population are screened for the presence of  Mycobacterium avium , ssp.  paratuberculosis  (MAP). 
     
     
       6. The method of  claim 1  wherein step 1 is performed using a bead chip. 
     
     
       7. The method of  claim 1  wherein step 1 comprises a field test. 
     
     
       8. The method of  claim 1  wherein step 1 comprises using a visual indicator. 
     
     
       9. The method of  claim 6  wherein the bead chip is useful for estimating breeding value in cattle.